PS.  Actually, there are other differences:

global_

_lib_name      mon_lib

_lib_version   5.39

_lib_update    06/11/12

So it's three months newer than the one you're using.  Have you run the CCP4 updater?

On Wed, Apr 10, 2013 at 3:38 PM, Nathaniel Echols <[email protected]> wrote:

Actually, I think there may be a problem with your CCP4 installation - the exact same file on my computer starts with "global_", while yours lacks the trailing underscore, and editing mine to match reproduces the crash.  With the underscore in place it should work (assuming nothing else has changed).

On Wed, Apr 10, 2013 at 3:28 PM, James Stroud <[email protected]> wrote:

Hi Nat,

On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:

The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled.  Is the script you're running mmtbx/dynamics/tst_sa.py?

Yes, that is the script I'm running.

Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback.

Here's the results:

% setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1

% cctbx.python ./tst_sa.py

Traceback (most recent call last):

  File "./tst_sa.py", line 267, in <module>

    exercise_1()

  File "./tst_sa.py", line 122, in exercise_1

    pi = get_pdb_inputs(pdb_str=pdb_str_1)

  File "./tst_sa.py", line 108, in get_pdb_inputs

    rama_potential=None, log = None)

  File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object

    mon_lib_srv = mmtbx.monomer_library.server.server()

  File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__

    list_cif = mon_lib_list_cif()

  File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif

    strict=strict)

  File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__

    self.cif = read_cif(file_name=self.path)

  File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif

    return iotbx.cif.reader(file_path=file_name, strict=False).model()

  File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__

    raise CifParserError(self.parser.parser_errors()[0])

CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1

    near global

     : unexpected input...

  expected one of : Actually dude, we didn't seem to be expecting anything here, or at least

I could not work out what I was expecting, like so many of us these days!

James

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